STY: Apply ruff/flake8-bugbear rule B007

DimitriPapadopoulos · effigies · commit ea421bcaa8cd · 2024-10-07T14:14:38.000-04:00
B007 Loop control variable not used within loop body
diff --git a/nipype/algorithms/mesh.py b/nipype/algorithms/mesh.py
@@ -244,7 +244,7 @@ def _run_interface(self, runtime):
         if self.inputs.weighting == "area":
             faces = vtk1.polys.to_array().reshape(-1, 4).astype(int)[:, 1:]
 
-            for i, p1 in enumerate(points2):
+            for i, _ in enumerate(points2):
                 # compute surfaces, set in weight
                 w = 0.0
                 point_faces = faces[(faces[:, :] == i).any(axis=1)]
diff --git a/nipype/algorithms/modelgen.py b/nipype/algorithms/modelgen.py
@@ -389,7 +389,7 @@ def _generate_standard_design(
             if hasattr(info, "conditions") and info.conditions is not None:
                 for cid, cond in enumerate(info.conditions):
                     sessinfo[i]["cond"].insert(cid, dict())
-                    sessinfo[i]["cond"][cid]["name"] = info.conditions[cid]
+                    sessinfo[i]["cond"][cid]["name"] = cond
                     scaled_onset = scale_timings(
                         info.onsets[cid],
                         self.inputs.input_units,
@@ -434,12 +434,12 @@ def _generate_standard_design(
                         sessinfo[i]["regress"][j]["name"] = info.regressor_names[j]
                     else:
                         sessinfo[i]["regress"][j]["name"] = "UR%d" % (j + 1)
-                    sessinfo[i]["regress"][j]["val"] = info.regressors[j]
+                    sessinfo[i]["regress"][j]["val"] = r
             sessinfo[i]["scans"] = functional_runs[i]
 
         if realignment_parameters is not None:
             for i, rp in enumerate(realignment_parameters):
-                mc = realignment_parameters[i]
+                mc = rp
                 for col in range(mc.shape[1]):
                     colidx = len(sessinfo[i]["regress"])
                     sessinfo[i]["regress"].insert(colidx, dict(name="", val=[]))
@@ -597,7 +597,7 @@ def _concatenate_info(self, infolist):
         for i, info in enumerate(infolist[1:]):
             # info.[conditions, tmod] remain the same
             if info.onsets:
-                for j, val in enumerate(info.onsets):
+                for j, _ in enumerate(info.onsets):
                     if self.inputs.input_units == "secs":
                         onsets = np.array(
                             info.onsets[j]
@@ -621,7 +621,7 @@ def _concatenate_info(self, infolist):
                         )
 
                 if hasattr(info, "amplitudes") and info.amplitudes:
-                    for j, val in enumerate(info.amplitudes):
+                    for j, _ in enumerate(info.amplitudes):
                         infoout.amplitudes[j].extend(info.amplitudes[j])
 
                 if hasattr(info, "pmod") and info.pmod:
@@ -633,7 +633,7 @@ def _concatenate_info(self, infolist):
             if hasattr(info, "regressors") and info.regressors:
                 # assumes same ordering of regressors across different
                 # runs and the same names for the regressors
-                for j, v in enumerate(info.regressors):
+                for j, _ in enumerate(info.regressors):
                     infoout.regressors[j].extend(info.regressors[j])
 
             # insert session regressors
diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py
@@ -351,7 +351,7 @@ def add_node_data(node_array, ntwk):
 def add_edge_data(edge_array, ntwk, above=0, below=0):
     edge_ntwk = ntwk.copy()
     data = {}
-    for x, row in enumerate(edge_array):
+    for x, row in enumerate(edge_array):  # noqa: B007
         for y in range(np.max(np.shape(edge_array[x]))):
             if edge_array[x, y] != 0:
                 data["value"] = edge_array[x, y]
@@ -550,14 +550,14 @@ def _run_interface(self, runtime):
         # stacks them together, and saves them in a MATLAB .mat file via Scipy
         global dicts
         dicts = list()
-        for idx, key in enumerate(dict_measures.keys()):
-            for idxd, keyd in enumerate(dict_measures[key].keys()):
+        for key, value in dict_measures:
+            for idxd, keyd in enumerate(value.keys()):
                 if idxd == 0:
                     nparraykeys = np.array(keyd)
-                    nparrayvalues = np.array(dict_measures[key][keyd])
+                    nparrayvalues = np.array(value[keyd])
                 else:
                     nparraykeys = np.append(nparraykeys, np.array(keyd))
-                    values = np.array(dict_measures[key][keyd])
+                    values = np.array(value[keyd])
                     nparrayvalues = np.append(nparrayvalues, values)
             nparray = np.vstack((nparraykeys, nparrayvalues))
             out_file = op.abspath(self._gen_outfilename(key, "mat"))
diff --git a/nipype/interfaces/cmtk/parcellation.py b/nipype/interfaces/cmtk/parcellation.py
@@ -598,7 +598,7 @@ def create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name):
     roid = np.asanyarray(roi.dataobj)
     assert roid.shape[0] == wmmask.shape[0]
     pg = nx.read_graphml(pgpath)
-    for brk, brv in pg.nodes(data=True):
+    for brk, brv in pg.nodes(data=True):  # noqa: B007
         if brv["dn_region"] == "cortical":
             iflogger.info(
                 "Subtracting region %s with intensity value %s",
diff --git a/nipype/interfaces/dcmstack.py b/nipype/interfaces/dcmstack.py
@@ -186,7 +186,7 @@ def _run_interface(self, runtime):
         stacks = dcmstack.parse_and_stack(src_paths)
 
         self.out_list = []
-        for key, stack in list(stacks.items()):
+        for stack in stacks.values():
             nw = NiftiWrapper(stack.to_nifti(embed_meta=True))
             const_meta = nw.meta_ext.get_class_dict(("global", "const"))
             out_path = self._get_out_path(const_meta)
diff --git a/nipype/interfaces/dipy/simulate.py b/nipype/interfaces/dipy/simulate.py
@@ -208,7 +208,7 @@ def _run_interface(self, runtime):
                 dirs = np.hstack((dirs, fd[msk > 0]))
 
         # Add random directions for isotropic components
-        for d in range(nballs):
+        for _ in range(nballs):
             fd = np.random.randn(nvox, 3)
             w = np.linalg.norm(fd, axis=1)
             fd[w < np.finfo(float).eps, ...] = np.array([1.0, 0.0, 0.0])
@@ -341,7 +341,7 @@ def _generate_gradients(ndirs=64, values=[1000, 3000], nb0s=1):
         bvecs = np.vstack((bvecs, vertices))
         bvals = np.hstack((bvals, v * np.ones(vertices.shape[0])))
 
-    for i in range(nb0s):
+    for _ in range(nb0s):
         bvals = bvals.tolist()
         bvals.insert(0, 0)
 
diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py
@@ -198,8 +198,8 @@ def _create_ev_files(
         # generate sections for conditions and other nuisance
         # regressors
         num_evs = [0, 0]
-        for field in ["cond", "regress"]:
-            for i, cond in enumerate(runinfo[field]):
+        for field in ("cond", "regress"):
+            for cond in runinfo[field]:
                 name = cond["name"]
                 evname.append(name)
                 evfname = os.path.join(
@@ -278,9 +278,7 @@ def _create_ev_files(
             contrastmask_element = load_template("feat_contrastmask_element.tcl")
             # add t/f contrast info
             ev_txt += contrast_header.substitute()
-            con_names = []
-            for j, con in enumerate(contrasts):
-                con_names.append(con[0])
+            con_names = [con[0] for con in contrasts]
             con_map = {}
             ftest_idx = []
             ttest_idx = []
@@ -364,7 +362,7 @@ def _run_interface(self, runtime):
         n_tcon = 0
         n_fcon = 0
         if isdefined(self.inputs.contrasts):
-            for i, c in enumerate(self.inputs.contrasts):
+            for c in self.inputs.contrasts:
                 if c[1] == "T":
                     n_tcon += 1
                 elif c[1] == "F":
@@ -421,7 +419,7 @@ def _list_outputs(self):
             outputs["ev_files"].insert(runno, [])
             evname = []
             for field in ["cond", "regress"]:
-                for i, cond in enumerate(runinfo[field]):
+                for cond in runinfo[field]:
                     name = cond["name"]
                     evname.append(name)
                     evfname = os.path.join(
@@ -1388,8 +1386,7 @@ def _run_interface(self, runtime):
             "",
             "/Matrix",
         ]
-        for i in range(self.inputs.num_copes):
-            mat_txt += ["1"]
+        mat_txt.extend("1" for _ in range(self.inputs.num_copes))
         mat_txt = "\n".join(mat_txt)
 
         con_txt = [
@@ -1411,16 +1408,15 @@ def _run_interface(self, runtime):
             "",
             "/Matrix",
         ]
-        for i in range(self.inputs.num_copes):
-            grp_txt += ["1"]
+        grp_txt.extend("1" for _ in range(self.inputs.num_copes))
         grp_txt = "\n".join(grp_txt)
 
         txt = {"design.mat": mat_txt, "design.con": con_txt, "design.grp": grp_txt}
 
         # write design files
-        for i, name in enumerate(["design.mat", "design.con", "design.grp"]):
+        for name, name_txt in txt.items():
             with open(os.path.join(cwd, name), "w") as f:
-                f.write(txt[name])
+                f.write(name_txt)
 
         return runtime
 
@@ -1559,7 +1555,7 @@ def _run_interface(self, runtime):
                 "",
                 "/Matrix",
             ]
-            for conidx, con in enumerate(self.inputs.contrasts):
+            for con in self.inputs.contrasts:
                 if con[1] == "F":
                     convals = np.zeros((ntcons, 1))
                     for tcon in con[2]:
diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
@@ -426,7 +426,7 @@ def _list_outputs(self):
             if len(self.inputs.in_files) > 1:
                 # for multi-image segmentation there is one corrected image
                 # per input
-                for val, f in enumerate(self.inputs.in_files):
+                for val, _ in enumerate(self.inputs.in_files):
                     # image numbering is 1-based
                     outputs["restored_image"].append(
                         self._gen_fname(
@@ -454,7 +454,7 @@ def _list_outputs(self):
             if len(self.inputs.in_files) > 1:
                 # for multi-image segmentation there is one bias field image
                 # per input
-                for val, f in enumerate(self.inputs.in_files):
+                for val, _ in enumerate(self.inputs.in_files):
                     # image numbering is 1-based
                     outputs["bias_field"].append(
                         self._gen_fname(
diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py
@@ -609,7 +609,7 @@ def _upload_to_s3(self, bucket, src, dst):
         # If src is a directory, collect files (this assumes dst is a dir too)
         if os.path.isdir(src):
             src_files = []
-            for root, dirs, files in os.walk(src):
+            for root, dirs, files in os.walk(src):  # noqa: B007
                 src_files.extend([os.path.join(root, fil) for fil in files])
             # Make the dst files have the dst folder as base dir
             dst_files = [os.path.join(dst, src_f.split(src)[1]) for src_f in src_files]
@@ -1393,7 +1393,7 @@ def __init__(self, templates, **kwargs):
 
         # Infer the infields and outfields from the template
         infields = []
-        for name, template in list(templates.items()):
+        for template in templates.values():
             for _, field_name, _, _ in string.Formatter().parse(template):
                 if field_name is not None:
                     field_name = re.match(r"\w+", field_name).group()
diff --git a/nipype/interfaces/mrtrix/convert.py b/nipype/interfaces/mrtrix/convert.py
@@ -100,9 +100,10 @@ def points_per_track(offset):
         ]  # Converts numpy array to list, removes the last value
         for idx, value in enumerate(nonfinite_list):
             if idx == 0:
-                track_points.append(nonfinite_list[idx])
+                track_points.append(value)
             else:
-                track_points.append(nonfinite_list[idx] - nonfinite_list[idx - 1] - 1)
+                track_points.append(value - last_value - 1)
+            last_value = value
         return track_points, nonfinite_list
 
     def track_gen(track_points):
diff --git a/nipype/interfaces/nipy/model.py b/nipype/interfaces/nipy/model.py
@@ -151,7 +151,7 @@ def _run_interface(self, runtime):
         onsets = []
         duration = []
 
-        for i, cond in enumerate(session_info[0]["cond"]):
+        for cond in session_info[0]["cond"]:
             onsets += cond["onset"]
             conditions += [cond["name"]] * len(cond["onset"])
             if len(cond["duration"]) == 1:
diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py
@@ -489,7 +489,7 @@ def _generate_job(self, prefix="", contents=None):
                     jobstring += "%s = {...\n" % (prefix)
                 else:
                     jobstring += "{...\n"
-                for i, val in enumerate(contents):
+                for val in contents:
                     if isinstance(val, np.ndarray):
                         jobstring += self._generate_job(prefix=None, contents=val)
                     elif isinstance(val, list):
diff --git a/nipype/interfaces/spm/preprocess.py b/nipype/interfaces/spm/preprocess.py
@@ -362,10 +362,10 @@ def _list_outputs(self):
 
         if resliced_all:
             outputs["out_files"] = []
-            for idx, imgf in enumerate(ensure_list(self.inputs.in_files)):
+            for imgf in ensure_list(self.inputs.in_files):
                 appliedvdm_run = []
                 if isinstance(imgf, list):
-                    for i, inner_imgf in enumerate(ensure_list(imgf)):
+                    for inner_imgf in ensure_list(imgf):
                         newfile = fname_presuffix(
                             inner_imgf, prefix=self.inputs.out_prefix
                         )
@@ -654,10 +654,10 @@ def _list_outputs(self):
 
             if resliced_all:
                 outputs["realigned_files"] = []
-                for idx, imgf in enumerate(ensure_list(self.inputs.in_files)):
+                for imgf in ensure_list(self.inputs.in_files):
                     realigned_run = []
                     if isinstance(imgf, list):
-                        for i, inner_imgf in enumerate(ensure_list(imgf)):
+                        for inner_imgf in ensure_list(imgf):
                             newfile = fname_presuffix(
                                 inner_imgf, prefix=self.inputs.out_prefix
                             )
@@ -922,10 +922,10 @@ def _list_outputs(self):
 
         if resliced_all:
             outputs["realigned_unwarped_files"] = []
-            for idx, imgf in enumerate(ensure_list(self.inputs.in_files)):
+            for imgf in ensure_list(self.inputs.in_files):
                 realigned_run = []
                 if isinstance(imgf, list):
-                    for i, inner_imgf in enumerate(ensure_list(imgf)):
+                    for inner_imgf in ensure_list(imgf):
                         newfile = fname_presuffix(
                             inner_imgf, prefix=self.inputs.out_prefix
                         )
@@ -1911,7 +1911,7 @@ def _list_outputs(self):
         n_classes = 5
         if isdefined(self.inputs.tissues):
             n_classes = len(self.inputs.tissues)
-        for i in range(n_classes):
+        for _ in range(n_classes):
             outputs["native_class_images"].append([])
             outputs["dartel_input_images"].append([])
             outputs["normalized_class_images"].append([])
@@ -2159,7 +2159,7 @@ def _list_outputs(self):
         n_classes = 5
         if isdefined(self.inputs.tissues):
             n_classes = len(self.inputs.tissues)
-        for i in range(n_classes):
+        for _ in range(n_classes):
             outputs["native_class_images"].append([])
             outputs["dartel_input_images"].append([])
             outputs["normalized_class_images"].append([])
diff --git a/nipype/pipeline/engine/tests/test_nodes.py b/nipype/pipeline/engine/tests/test_nodes.py
@@ -181,7 +181,7 @@ def func1(in1):
     )
     mapnode.inputs.in1 = [1, 2]
 
-    for idx, node in mapnode._make_nodes():
+    for idx, node in mapnode._make_nodes():  # noqa: B007
         for attr in ("overwrite", "run_without_submitting", "plugin_args"):
             assert getattr(node, attr) == getattr(mapnode, attr)
         for attr in ("_n_procs", "_mem_gb"):
diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py
@@ -537,7 +537,7 @@ def _write_detailed_dot(graph, dotfilename):
             + ["}"]
         )
         outports = []
-        for u, v, d in graph.out_edges(nbunch=n, data=True):
+        for u, v, d in graph.out_edges(nbunch=n, data=True):  # noqa: B007
             for cd in d["connect"]:
                 if isinstance(cd[0], (str, bytes)):
                     outport = cd[0]
@@ -1604,7 +1604,7 @@ def write_workflow_prov(graph, filename=None, format="all"):
 
     # add dependencies (edges)
     # Process->Process
-    for idx, edgeinfo in enumerate(graph.in_edges()):
+    for edgeinfo in graph.in_edges():
         ps.g.wasStartedBy(
             processes[list(nodes).index(edgeinfo[1])],
             starter=processes[list(nodes).index(edgeinfo[0])],
diff --git a/nipype/pipeline/engine/workflows.py b/nipype/pipeline/engine/workflows.py
@@ -232,7 +232,7 @@ def connect(self, *args, **kwargs):
             raise Exception("\n".join(["Some connections were not found"] + infostr))
 
         # turn functions into strings
-        for srcnode, destnode, connects in connection_list:
+        for srcnode, destnode, connects in connection_list:  # noqa: B007
             for idx, (src, dest) in enumerate(connects):
                 if isinstance(src, tuple) and not isinstance(src[1], (str, bytes)):
                     function_source = getsource(src[1])
@@ -702,9 +702,9 @@ def getname(u, i):
 
         json_dict = []
         for i, node in enumerate(nodes):
-            imports = []
-            for u, v in graph.in_edges(nbunch=node):
-                imports.append(getname(u, nodes.index(u)))
+            imports = [
+                getname(u, nodes.index(u)) for u, v in graph.in_edges(nbunch=node)
+            ]
             json_dict.append(
                 dict(name=getname(node, i), size=1, group=groups[i], imports=imports)
             )
diff --git a/nipype/pipeline/plugins/sgegraph.py b/nipype/pipeline/plugins/sgegraph.py
@@ -80,7 +80,7 @@ def make_job_name(jobnumber, nodeslist):
         if (
             self._dont_resubmit_completed_jobs
         ):  # A future parameter for controlling this behavior could be added here
-            for idx, pyscript in enumerate(pyfiles):
+            for idx, pyscript in enumerate(pyfiles):  # noqa: B007
                 node = nodes[idx]
                 node_status_done = node_completed_status(node)
 
diff --git a/nipype/pipeline/plugins/slurmgraph.py b/nipype/pipeline/plugins/slurmgraph.py
@@ -80,7 +80,7 @@ def make_job_name(jobnumber, nodeslist):
         if (
             self._dont_resubmit_completed_jobs
         ):  # A future parameter for controlling this behavior could be added here
-            for idx, pyscript in enumerate(pyfiles):
+            for idx, pyscript in enumerate(pyfiles):  # noqa: B007
                 node = nodes[idx]
                 node_status_done = node_completed_status(node)
 
diff --git a/nipype/sphinxext/plot_workflow.py b/nipype/sphinxext/plot_workflow.py
diff --git a/nipype/testing/utils.py b/nipype/testing/utils.py
diff --git a/nipype/utils/draw_gantt_chart.py b/nipype/utils/draw_gantt_chart.py
diff --git a/nipype/utils/matlabtools.py b/nipype/utils/matlabtools.py
diff --git a/nipype/utils/provenance.py b/nipype/utils/provenance.py
